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Crystal structure of a chemically synthesized 203 amino acid 'covalent dimer' HIV-1 protease molecule

Analyse Crystal structure of a chemically synthesized 203 amino acid 'covalent dimer'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O40
Type: protein
Length: 203 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Covalent dimer HIV-1 protease
EC: 3.4.23.16
Ligands: 2NC
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Covalent dimer HIV-1 protease (EC 3.4.23.16)	protein	203	5% helix, 51% strand	—

Ligands and binding sites

2NC · N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	362	0.71	0.83	41	2NC

Modifications

Observed in the structure: 11 modified (nonstandard, alkylation).

Compared structures

2O40 · Crystal Structure of a Chemically Synthesized 203 Amino Acid 'Covalent Dimer' HIV-1… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 2O40 · PDBe 2O40

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